Genome sequence of Janthinobacterium sp. strain PAMC 25724, isolated from alpine glacier cryoconite.
ABSTRACT The draft genome of Janthinobacterium sp. strain PAMC 25724, which is a violacein-producing psychrotolerant bacterium, was determined. The strain was isolated from glacier cryoconite of the Alps mountain permafrost region. The sequence will allow identification and characterization of the genetic determination of its cold-adaptive properties.
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ABSTRACT: The database of Clusters of Orthologous Groups of proteins (COGs), which represents an attempt on a phylogenetic classification of the proteins encoded in complete genomes, currently consists of 2791 COGs including 45 350 proteins from 30 genomes of bacteria, archaea and the yeast Saccharomyces cerevisiae (http://www.ncbi.nlm.nih.gov/COG). In addition, a supplement to the COGs is available, in which proteins encoded in the genomes of two multicellular eukaryotes, the nematode Caenorhabditis elegans and the fruit fly Drosophila melanogaster, and shared with bacteria and/or archaea were included. The new features added to the COG database include information pages with structural and functional details on each COG and literature references, improvements of the COGNITOR program that is used to fit new proteins into the COGs, and classification of genomes and COGs constructed by using principal component analysis.Nucleic Acids Research 02/2001; · 8.28 Impact Factor
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ABSTRACT: The structures of janthinocins A, B and C, three novel macrocyclic peptide lactone antibiotics isolated from fermentations of Janthinobacterium lividum, were determined. The janthinocins are of particular interest because they contain three amino acid residues that have not previously been reported in natural products: Each contains erythro-beta-hydroxy-D-leucine while janthinocins A and B also contain beta-hydroxytryptophan and beta-ketotryptophan, respectively.The Journal of Antibiotics 09/1990; 43(8):920-30. · 2.19 Impact Factor
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ABSTRACT: We report on the quality of a whole-genome assembly of Drosophila melanogaster and the nature of the computer algorithms that accomplished it. Three independent external data sources essentially agree with and support the assembly's sequence and ordering of contigs across the euchromatic portion of the genome. In addition, there are isolated contigs that we believe represent nonrepetitive pockets within the heterochromatin of the centromeres. Comparison with a previously sequenced 2.9- megabase region indicates that sequencing accuracy within nonrepetitive segments is greater than 99. 99% without manual curation. As such, this initial reconstruction of the Drosophila sequence should be of substantial value to the scientific community.Science 04/2000; 287(5461):2196-204. · 31.03 Impact Factor
Genome Sequence of Janthinobacterium sp. Strain PAMC 25724,
Isolated from Alpine Glacier Cryoconite
Su Jin Kim,aSeung Chul Shin,bSoon Gyu Hong,bYung Mi Lee,bHyoungseok Lee,bJungeun Lee,bIn-Geol Choi,aand Hyun Parkb
College of Life Sciences and Biotechnology, Korea University, Seongbuk-gu, Seoul, South Korea,aand Korea Polar Research Institute, Yeonsu-gu, Incheon, South Koreab
Thedraftgenomeof Janthinobacterium sp.strainPAMC25724,whichisaviolacein-producingpsychrotolerantbacterium,was
monly isolated from the microbiota of soils and water of rivers,
soil (4, 7). Janthinobacterium sp. is one of the most common pur-
violacein (6), and it is suggested that the inhibitory effects of the
PAMC 25724 was isolated from glacier cryoconite of the Alps
mountain range, Austria (47°04=N, 12°41=E).
The genome of Janthinobacterium sp. PAMC 25724 was ana-
lyzed using a combined approach with the 454 GS FLX Titanium
system (Roche Diagnostics, Branford, CT) with an 8-kb paired-
end library (111,434 reads) and the Illumina GAIIx (San Diego,
GS FLX sequencing achieved about 8.7-fold coverage, while 208-
fold read coverage was achieved by Illumina paired-end sequenc-
ing. The reads generated by the Illumina GAIIx and the 454 GS
FLX Titanium were assembled using Celera assembler 6.1 (5).
(3), the rapid annotations using subsystems technology (RAST)
server (1), and the NCBI COG database (8). The draft genome se-
quence of Janthinobacterium sp. PAMC 25724 includes 4,985,247
5S rRNA genes, one 23S rRNA gene, and one 16S rRNA gene were
predicted in the draft genome. Approximately 84.9% of nucleotides
were predicted as protein-coding regions, and 73.7% (3,197) of the
Janthinobacterium sp. Marseille (score, 537), Herminiimonas arseni-
coxydans (score, 422), and Oxalobacter formigenes OXCC13 (score,
he genus Janthinobacterium includes violacein-producing,
Gram-negative, motile, rod-shaped bacteria that are com-
in this paper is the first version, AHHB01000000.
This work was supported by a Functional Genomics on Polar Organisms
grant (PE12020) funded by the Korea Polar Research Institute (KOPRI).
technology. BMC Genomics 9:75.
2. Brucker RM, et al. 2008. Amphibian chemical defense: antifungal metab-
Plethodon cinereus. J. Chem. Ecol. 34:1422–1429.
3. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. 1999. Improved
4. Johnson JH, Tymiak AA, Bolgar MS. 1990. Janthinocins A, B and C, novel
peptide lactone antibiotics produced by Janthinobacterium lividum. II.
Structure elucidation. J. Antibiot. (Tokyo) 43:920–930.
5. Myers EW, et al. 2000. A whole-genome assembly of Drosophila. Science
6. Pantanella F, et al. 2007. Violacein and biofilm production in Janthino-
bacterium lividum. J. Appl. Microbiol. 102:992–999.
8. Tatusov RL, et al. 2001. The COG database: new developments in phylo-
genetic classification of proteins from complete genomes. Nucleic Acids
Received 19 January 2012 Accepted 2 February 2012
Address correspondence to Hyun Park, email@example.com, or In-Geol Choi,
S.J.K. and S.C.S. contributed equally to this publication.
Copyright © 2012, American Society for Microbiology. All Rights Reserved.
jb.asm.org0021-9193/12/$12.00 Journal of Bacteriology p. 2096